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SIB Swiss Institute of Bioinformatics swiss-pdb viewer (aka deepview)
Swiss Pdb Viewer (Aka Deepview), supplied by SIB Swiss Institute of Bioinformatics, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Microscopy:

Article Title: Hexameric tetrahedral RNA nanostructures
Article Snippet: A UA-handle three way junction (Protein Database (PDB) identification: 2AW4; nts 2090-2095, 2194-2201, 2220-2229) was then inserted into appropriate ring monomers, after which a helical segment was inserted to connect the junctions using SWISS PDB-VIEWER (The SIB Swiss Institute of Bioinformatics, available on the website for ExPASy Bioinformatics Resource Portal).

Article Title: The intrinsically disordered region of coronins fine-tunes oligomerization and actin polymerization.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Gromacs 5.1.2 Open source http://www.gromacs.org/ Swiss-Pdb Viewer (aka DeepView) SIB Swiss Institute of Bioinformatics http://www.expasy.org/spdbv/ CCBuilder 2.0 Open source http://coiledcoils.chm.bris.ac.uk/ ccbuilder2/builder PyMOL Schrödinger https://www.pymol.org/ Python for file processing CWI, the Netherlands https://www.python.org/ MATLAB vR2020b The MathWorks, Natick, MA https://www.mathworks.com/ PULCHRA Open Source http://cssb.bio.ogy.gatech.edu/skolnick/ files/PULCHRA Other Glass based dish, 27mm Thermo ScientificTM Cat#150682 Microscope circular cover glass, thickness No.1.5, 25mm diameter Marienfeld Superior, Germany Cat#0112650 Microscope cover glass, thickness No.1.5 size: 24x50 mm Marienfeld Superior, Germany Cat#0102222 0.5mm Zirconia/Silica beads Biospec Products Cat#110791052 HisTrap HP column Cytiva Product No: 17524802 HiLoad 16/600 Superdex 200 pg column Cytiva Product No: 28989335 Superdex 200 Increase 10/300 GL column Cytiva Product No: 28990944 Amicon Ultra-15 Centrifugal Filter Unit Merk Millipore Cat#UFC901024 HiPrep 16/60 Sephacryl S-300 HR column Cytiva Product No: 17116701 Carbon support film 200 Mesh, copper Electron Microscopy Sciences Cat#CF200-Cu 1mm path length cuvette Hellma Analytics Article No:100-1-40 TLA-100 Fixed-Angle Rotor Beckman Coulter 343840 Plastic flow cell chamber (sticky-slide VI0.4) Ibidi GmbH Cat#80608

Article Title: The β-chain mutation p.Trp433Stop impairs fibrinogen secretion: A novel nonsense mutation associated with hypofibrinogenemia.
Article Snippet: Fibrinogen, a hexameric glycoprotein composed of Aα, Bβ, and γ chains, is the most abundant clotting factor in human circulation, and it has a multitude of functions, including platelet aggregation, primary and secondary hemostasis, and fibrinolysis.1 Congenital fibrinogen disorders are divided into two categories: type I, consisting of quantitative defects (afibrinogenemia or hypofibrinogenemia) characterized by absent or low plasma fibrinogen antigen and activity levels, and type II, consisting of qualitative defects Received: 8 December 2020 | Revised: 12 May 2021 | Accepted: 27 May 2021 DOI: 10.1111/ijlh.13632

Article Title: Protocol to identify multiple protein targets and therapeutic compounds using an in silico polypharmacological approach
Article Snippet: SWISS PDB Viewer , SIB Swiss Institute of Bioinformatics , https://spdbv.unil.ch/refs.html.

Article Title: Hexameric tetrahedral RNA nanostructures
Article Snippet: A three-dimensional model of the tetrahedral scaffold was manually constructed using SWISS PDB-VIEWER (The SIB Swiss Institute of Bioinformatics, available on the website for ExPASy Bioinformatics Resource Portal) and existing RNA structural data available in the PDB.

Article Title: Ubiquitin Modification by the E3 Ligase/ADP-ribosyltransferase Dtx3L/Parp9
Article Snippet: Swiss-PDB Viewer , The SIB Swiss Institute of Bioinformatics , N/A.

Article Title: A novel fibrinogen gamma-chain mutation, p.Cys165Arg, causes disruption of the γ165Cys-Bβ227Cys disulfide bond and ultimately leads to hypofibrinogenemia.
Article Snippet: Background: Congenital hypofibrinogenemia is a type of hereditary disease characterized by impaired fibrinogen synthesis and/or secretion induced by mutations in the fibrinogen gene.. Objectives: We investigated the phenotypes, genotypes, and pathogenesis of congenital hypofibrinogenemia in

Article Title: Genetic analysis of a pedigree with hereditary coagulation factor XI deficiency
Article Snippet: To identify potential mutations of F11 gene in a family with hereditary coagulation factor XI (FXI) deficiency and explore the molecular pathogenesis.. The FXI activity and FXI antigen were tested with clotting assay and ELISA, respectively.. The FXI gene was amplified by PCR with direct sequencing.

Electron Microscopy:

Article Title: Hexameric tetrahedral RNA nanostructures
Article Snippet: A UA-handle three way junction (Protein Database (PDB) identification: 2AW4; nts 2090-2095, 2194-2201, 2220-2229) was then inserted into appropriate ring monomers, after which a helical segment was inserted to connect the junctions using SWISS PDB-VIEWER (The SIB Swiss Institute of Bioinformatics, available on the website for ExPASy Bioinformatics Resource Portal).

Article Title: The intrinsically disordered region of coronins fine-tunes oligomerization and actin polymerization.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Gromacs 5.1.2 Open source http://www.gromacs.org/ Swiss-Pdb Viewer (aka DeepView) SIB Swiss Institute of Bioinformatics http://www.expasy.org/spdbv/ CCBuilder 2.0 Open source http://coiledcoils.chm.bris.ac.uk/ ccbuilder2/builder PyMOL Schrödinger https://www.pymol.org/ Python for file processing CWI, the Netherlands https://www.python.org/ MATLAB vR2020b The MathWorks, Natick, MA https://www.mathworks.com/ PULCHRA Open Source http://cssb.bio.ogy.gatech.edu/skolnick/ files/PULCHRA Other Glass based dish, 27mm Thermo ScientificTM Cat#150682 Microscope circular cover glass, thickness No.1.5, 25mm diameter Marienfeld Superior, Germany Cat#0112650 Microscope cover glass, thickness No.1.5 size: 24x50 mm Marienfeld Superior, Germany Cat#0102222 0.5mm Zirconia/Silica beads Biospec Products Cat#110791052 HisTrap HP column Cytiva Product No: 17524802 HiLoad 16/600 Superdex 200 pg column Cytiva Product No: 28989335 Superdex 200 Increase 10/300 GL column Cytiva Product No: 28990944 Amicon Ultra-15 Centrifugal Filter Unit Merk Millipore Cat#UFC901024 HiPrep 16/60 Sephacryl S-300 HR column Cytiva Product No: 17116701 Carbon support film 200 Mesh, copper Electron Microscopy Sciences Cat#CF200-Cu 1mm path length cuvette Hellma Analytics Article No:100-1-40 TLA-100 Fixed-Angle Rotor Beckman Coulter 343840 Plastic flow cell chamber (sticky-slide VI0.4) Ibidi GmbH Cat#80608

Article Title: The β-chain mutation p.Trp433Stop impairs fibrinogen secretion: A novel nonsense mutation associated with hypofibrinogenemia.
Article Snippet: Fibrinogen, a hexameric glycoprotein composed of Aα, Bβ, and γ chains, is the most abundant clotting factor in human circulation, and it has a multitude of functions, including platelet aggregation, primary and secondary hemostasis, and fibrinolysis.1 Congenital fibrinogen disorders are divided into two categories: type I, consisting of quantitative defects (afibrinogenemia or hypofibrinogenemia) characterized by absent or low plasma fibrinogen antigen and activity levels, and type II, consisting of qualitative defects Received: 8 December 2020 | Revised: 12 May 2021 | Accepted: 27 May 2021 DOI: 10.1111/ijlh.13632

Article Title: Protocol to identify multiple protein targets and therapeutic compounds using an in silico polypharmacological approach
Article Snippet: SWISS PDB Viewer , SIB Swiss Institute of Bioinformatics , https://spdbv.unil.ch/refs.html.

Article Title: Hexameric tetrahedral RNA nanostructures
Article Snippet: A three-dimensional model of the tetrahedral scaffold was manually constructed using SWISS PDB-VIEWER (The SIB Swiss Institute of Bioinformatics, available on the website for ExPASy Bioinformatics Resource Portal) and existing RNA structural data available in the PDB.

Article Title: Ubiquitin Modification by the E3 Ligase/ADP-ribosyltransferase Dtx3L/Parp9
Article Snippet: Swiss-PDB Viewer , The SIB Swiss Institute of Bioinformatics , N/A.

Article Title: A novel fibrinogen gamma-chain mutation, p.Cys165Arg, causes disruption of the γ165Cys-Bβ227Cys disulfide bond and ultimately leads to hypofibrinogenemia.
Article Snippet: Background: Congenital hypofibrinogenemia is a type of hereditary disease characterized by impaired fibrinogen synthesis and/or secretion induced by mutations in the fibrinogen gene.. Objectives: We investigated the phenotypes, genotypes, and pathogenesis of congenital hypofibrinogenemia in

Article Title: Genetic analysis of a pedigree with hereditary coagulation factor XI deficiency
Article Snippet: To identify potential mutations of F11 gene in a family with hereditary coagulation factor XI (FXI) deficiency and explore the molecular pathogenesis.. The FXI activity and FXI antigen were tested with clotting assay and ELISA, respectively.. The FXI gene was amplified by PCR with direct sequencing.

Software:

Article Title: Hexameric tetrahedral RNA nanostructures
Article Snippet: A UA-handle three way junction (Protein Database (PDB) identification: 2AW4; nts 2090-2095, 2194-2201, 2220-2229) was then inserted into appropriate ring monomers, after which a helical segment was inserted to connect the junctions using SWISS PDB-VIEWER (The SIB Swiss Institute of Bioinformatics, available on the website for ExPASy Bioinformatics Resource Portal).

Article Title: The intrinsically disordered region of coronins fine-tunes oligomerization and actin polymerization.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Gromacs 5.1.2 Open source http://www.gromacs.org/ Swiss-Pdb Viewer (aka DeepView) SIB Swiss Institute of Bioinformatics http://www.expasy.org/spdbv/ CCBuilder 2.0 Open source http://coiledcoils.chm.bris.ac.uk/ ccbuilder2/builder PyMOL Schrödinger https://www.pymol.org/ Python for file processing CWI, the Netherlands https://www.python.org/ MATLAB vR2020b The MathWorks, Natick, MA https://www.mathworks.com/ PULCHRA Open Source http://cssb.bio.ogy.gatech.edu/skolnick/ files/PULCHRA Other Glass based dish, 27mm Thermo ScientificTM Cat#150682 Microscope circular cover glass, thickness No.1.5, 25mm diameter Marienfeld Superior, Germany Cat#0112650 Microscope cover glass, thickness No.1.5 size: 24x50 mm Marienfeld Superior, Germany Cat#0102222 0.5mm Zirconia/Silica beads Biospec Products Cat#110791052 HisTrap HP column Cytiva Product No: 17524802 HiLoad 16/600 Superdex 200 pg column Cytiva Product No: 28989335 Superdex 200 Increase 10/300 GL column Cytiva Product No: 28990944 Amicon Ultra-15 Centrifugal Filter Unit Merk Millipore Cat#UFC901024 HiPrep 16/60 Sephacryl S-300 HR column Cytiva Product No: 17116701 Carbon support film 200 Mesh, copper Electron Microscopy Sciences Cat#CF200-Cu 1mm path length cuvette Hellma Analytics Article No:100-1-40 TLA-100 Fixed-Angle Rotor Beckman Coulter 343840 Plastic flow cell chamber (sticky-slide VI0.4) Ibidi GmbH Cat#80608

Article Title: The β-chain mutation p.Trp433Stop impairs fibrinogen secretion: A novel nonsense mutation associated with hypofibrinogenemia.
Article Snippet: Fibrinogen, a hexameric glycoprotein composed of Aα, Bβ, and γ chains, is the most abundant clotting factor in human circulation, and it has a multitude of functions, including platelet aggregation, primary and secondary hemostasis, and fibrinolysis.1 Congenital fibrinogen disorders are divided into two categories: type I, consisting of quantitative defects (afibrinogenemia or hypofibrinogenemia) characterized by absent or low plasma fibrinogen antigen and activity levels, and type II, consisting of qualitative defects Received: 8 December 2020 | Revised: 12 May 2021 | Accepted: 27 May 2021 DOI: 10.1111/ijlh.13632

Article Title: Protocol to identify multiple protein targets and therapeutic compounds using an in silico polypharmacological approach
Article Snippet: SWISS PDB Viewer , SIB Swiss Institute of Bioinformatics , https://spdbv.unil.ch/refs.html.

Article Title: Hexameric tetrahedral RNA nanostructures
Article Snippet: A three-dimensional model of the tetrahedral scaffold was manually constructed using SWISS PDB-VIEWER (The SIB Swiss Institute of Bioinformatics, available on the website for ExPASy Bioinformatics Resource Portal) and existing RNA structural data available in the PDB.

Article Title: Ubiquitin Modification by the E3 Ligase/ADP-ribosyltransferase Dtx3L/Parp9
Article Snippet: Swiss-PDB Viewer , The SIB Swiss Institute of Bioinformatics , N/A.

Article Title: A novel fibrinogen gamma-chain mutation, p.Cys165Arg, causes disruption of the γ165Cys-Bβ227Cys disulfide bond and ultimately leads to hypofibrinogenemia.
Article Snippet: Background: Congenital hypofibrinogenemia is a type of hereditary disease characterized by impaired fibrinogen synthesis and/or secretion induced by mutations in the fibrinogen gene.. Objectives: We investigated the phenotypes, genotypes, and pathogenesis of congenital hypofibrinogenemia in

Article Title: Genetic analysis of a pedigree with hereditary coagulation factor XI deficiency
Article Snippet: To identify potential mutations of F11 gene in a family with hereditary coagulation factor XI (FXI) deficiency and explore the molecular pathogenesis.. The FXI activity and FXI antigen were tested with clotting assay and ELISA, respectively.. The FXI gene was amplified by PCR with direct sequencing.

Construct:

Article Title: Hexameric tetrahedral RNA nanostructures
Article Snippet: A UA-handle three way junction (Protein Database (PDB) identification: 2AW4; nts 2090-2095, 2194-2201, 2220-2229) was then inserted into appropriate ring monomers, after which a helical segment was inserted to connect the junctions using SWISS PDB-VIEWER (The SIB Swiss Institute of Bioinformatics, available on the website for ExPASy Bioinformatics Resource Portal).

Article Title: The intrinsically disordered region of coronins fine-tunes oligomerization and actin polymerization.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Gromacs 5.1.2 Open source http://www.gromacs.org/ Swiss-Pdb Viewer (aka DeepView) SIB Swiss Institute of Bioinformatics http://www.expasy.org/spdbv/ CCBuilder 2.0 Open source http://coiledcoils.chm.bris.ac.uk/ ccbuilder2/builder PyMOL Schrödinger https://www.pymol.org/ Python for file processing CWI, the Netherlands https://www.python.org/ MATLAB vR2020b The MathWorks, Natick, MA https://www.mathworks.com/ PULCHRA Open Source http://cssb.bio.ogy.gatech.edu/skolnick/ files/PULCHRA Other Glass based dish, 27mm Thermo ScientificTM Cat#150682 Microscope circular cover glass, thickness No.1.5, 25mm diameter Marienfeld Superior, Germany Cat#0112650 Microscope cover glass, thickness No.1.5 size: 24x50 mm Marienfeld Superior, Germany Cat#0102222 0.5mm Zirconia/Silica beads Biospec Products Cat#110791052 HisTrap HP column Cytiva Product No: 17524802 HiLoad 16/600 Superdex 200 pg column Cytiva Product No: 28989335 Superdex 200 Increase 10/300 GL column Cytiva Product No: 28990944 Amicon Ultra-15 Centrifugal Filter Unit Merk Millipore Cat#UFC901024 HiPrep 16/60 Sephacryl S-300 HR column Cytiva Product No: 17116701 Carbon support film 200 Mesh, copper Electron Microscopy Sciences Cat#CF200-Cu 1mm path length cuvette Hellma Analytics Article No:100-1-40 TLA-100 Fixed-Angle Rotor Beckman Coulter 343840 Plastic flow cell chamber (sticky-slide VI0.4) Ibidi GmbH Cat#80608

Article Title: The β-chain mutation p.Trp433Stop impairs fibrinogen secretion: A novel nonsense mutation associated with hypofibrinogenemia.
Article Snippet: Fibrinogen, a hexameric glycoprotein composed of Aα, Bβ, and γ chains, is the most abundant clotting factor in human circulation, and it has a multitude of functions, including platelet aggregation, primary and secondary hemostasis, and fibrinolysis.1 Congenital fibrinogen disorders are divided into two categories: type I, consisting of quantitative defects (afibrinogenemia or hypofibrinogenemia) characterized by absent or low plasma fibrinogen antigen and activity levels, and type II, consisting of qualitative defects Received: 8 December 2020 | Revised: 12 May 2021 | Accepted: 27 May 2021 DOI: 10.1111/ijlh.13632

Article Title: Protocol to identify multiple protein targets and therapeutic compounds using an in silico polypharmacological approach
Article Snippet: SWISS PDB Viewer , SIB Swiss Institute of Bioinformatics , https://spdbv.unil.ch/refs.html.

Article Title: Hexameric tetrahedral RNA nanostructures
Article Snippet: A three-dimensional model of the tetrahedral scaffold was manually constructed using SWISS PDB-VIEWER (The SIB Swiss Institute of Bioinformatics, available on the website for ExPASy Bioinformatics Resource Portal) and existing RNA structural data available in the PDB.

Article Title: Ubiquitin Modification by the E3 Ligase/ADP-ribosyltransferase Dtx3L/Parp9
Article Snippet: Swiss-PDB Viewer , The SIB Swiss Institute of Bioinformatics , N/A.

Article Title: A novel fibrinogen gamma-chain mutation, p.Cys165Arg, causes disruption of the γ165Cys-Bβ227Cys disulfide bond and ultimately leads to hypofibrinogenemia.
Article Snippet: Background: Congenital hypofibrinogenemia is a type of hereditary disease characterized by impaired fibrinogen synthesis and/or secretion induced by mutations in the fibrinogen gene.. Objectives: We investigated the phenotypes, genotypes, and pathogenesis of congenital hypofibrinogenemia in

Article Title: Genetic analysis of a pedigree with hereditary coagulation factor XI deficiency
Article Snippet: To identify potential mutations of F11 gene in a family with hereditary coagulation factor XI (FXI) deficiency and explore the molecular pathogenesis.. The FXI activity and FXI antigen were tested with clotting assay and ELISA, respectively.. The FXI gene was amplified by PCR with direct sequencing.

Mutagenesis:

Article Title: Hexameric tetrahedral RNA nanostructures
Article Snippet: A UA-handle three way junction (Protein Database (PDB) identification: 2AW4; nts 2090-2095, 2194-2201, 2220-2229) was then inserted into appropriate ring monomers, after which a helical segment was inserted to connect the junctions using SWISS PDB-VIEWER (The SIB Swiss Institute of Bioinformatics, available on the website for ExPASy Bioinformatics Resource Portal).

Article Title: The intrinsically disordered region of coronins fine-tunes oligomerization and actin polymerization.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Gromacs 5.1.2 Open source http://www.gromacs.org/ Swiss-Pdb Viewer (aka DeepView) SIB Swiss Institute of Bioinformatics http://www.expasy.org/spdbv/ CCBuilder 2.0 Open source http://coiledcoils.chm.bris.ac.uk/ ccbuilder2/builder PyMOL Schrödinger https://www.pymol.org/ Python for file processing CWI, the Netherlands https://www.python.org/ MATLAB vR2020b The MathWorks, Natick, MA https://www.mathworks.com/ PULCHRA Open Source http://cssb.bio.ogy.gatech.edu/skolnick/ files/PULCHRA Other Glass based dish, 27mm Thermo ScientificTM Cat#150682 Microscope circular cover glass, thickness No.1.5, 25mm diameter Marienfeld Superior, Germany Cat#0112650 Microscope cover glass, thickness No.1.5 size: 24x50 mm Marienfeld Superior, Germany Cat#0102222 0.5mm Zirconia/Silica beads Biospec Products Cat#110791052 HisTrap HP column Cytiva Product No: 17524802 HiLoad 16/600 Superdex 200 pg column Cytiva Product No: 28989335 Superdex 200 Increase 10/300 GL column Cytiva Product No: 28990944 Amicon Ultra-15 Centrifugal Filter Unit Merk Millipore Cat#UFC901024 HiPrep 16/60 Sephacryl S-300 HR column Cytiva Product No: 17116701 Carbon support film 200 Mesh, copper Electron Microscopy Sciences Cat#CF200-Cu 1mm path length cuvette Hellma Analytics Article No:100-1-40 TLA-100 Fixed-Angle Rotor Beckman Coulter 343840 Plastic flow cell chamber (sticky-slide VI0.4) Ibidi GmbH Cat#80608

Article Title: The β-chain mutation p.Trp433Stop impairs fibrinogen secretion: A novel nonsense mutation associated with hypofibrinogenemia.
Article Snippet: Fibrinogen, a hexameric glycoprotein composed of Aα, Bβ, and γ chains, is the most abundant clotting factor in human circulation, and it has a multitude of functions, including platelet aggregation, primary and secondary hemostasis, and fibrinolysis.1 Congenital fibrinogen disorders are divided into two categories: type I, consisting of quantitative defects (afibrinogenemia or hypofibrinogenemia) characterized by absent or low plasma fibrinogen antigen and activity levels, and type II, consisting of qualitative defects Received: 8 December 2020 | Revised: 12 May 2021 | Accepted: 27 May 2021 DOI: 10.1111/ijlh.13632

Article Title: Protocol to identify multiple protein targets and therapeutic compounds using an in silico polypharmacological approach
Article Snippet: SWISS PDB Viewer , SIB Swiss Institute of Bioinformatics , https://spdbv.unil.ch/refs.html.

Article Title: Hexameric tetrahedral RNA nanostructures
Article Snippet: A three-dimensional model of the tetrahedral scaffold was manually constructed using SWISS PDB-VIEWER (The SIB Swiss Institute of Bioinformatics, available on the website for ExPASy Bioinformatics Resource Portal) and existing RNA structural data available in the PDB.

Article Title: Ubiquitin Modification by the E3 Ligase/ADP-ribosyltransferase Dtx3L/Parp9
Article Snippet: Swiss-PDB Viewer , The SIB Swiss Institute of Bioinformatics , N/A.

Article Title: A novel fibrinogen gamma-chain mutation, p.Cys165Arg, causes disruption of the γ165Cys-Bβ227Cys disulfide bond and ultimately leads to hypofibrinogenemia.
Article Snippet: Background: Congenital hypofibrinogenemia is a type of hereditary disease characterized by impaired fibrinogen synthesis and/or secretion induced by mutations in the fibrinogen gene.. Objectives: We investigated the phenotypes, genotypes, and pathogenesis of congenital hypofibrinogenemia in

Article Title: Genetic analysis of a pedigree with hereditary coagulation factor XI deficiency
Article Snippet: To identify potential mutations of F11 gene in a family with hereditary coagulation factor XI (FXI) deficiency and explore the molecular pathogenesis.. The FXI activity and FXI antigen were tested with clotting assay and ELISA, respectively.. The FXI gene was amplified by PCR with direct sequencing.

FLAG-tag:

Article Title: Hexameric tetrahedral RNA nanostructures
Article Snippet: A UA-handle three way junction (Protein Database (PDB) identification: 2AW4; nts 2090-2095, 2194-2201, 2220-2229) was then inserted into appropriate ring monomers, after which a helical segment was inserted to connect the junctions using SWISS PDB-VIEWER (The SIB Swiss Institute of Bioinformatics, available on the website for ExPASy Bioinformatics Resource Portal).

Article Title: The intrinsically disordered region of coronins fine-tunes oligomerization and actin polymerization.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Gromacs 5.1.2 Open source http://www.gromacs.org/ Swiss-Pdb Viewer (aka DeepView) SIB Swiss Institute of Bioinformatics http://www.expasy.org/spdbv/ CCBuilder 2.0 Open source http://coiledcoils.chm.bris.ac.uk/ ccbuilder2/builder PyMOL Schrödinger https://www.pymol.org/ Python for file processing CWI, the Netherlands https://www.python.org/ MATLAB vR2020b The MathWorks, Natick, MA https://www.mathworks.com/ PULCHRA Open Source http://cssb.bio.ogy.gatech.edu/skolnick/ files/PULCHRA Other Glass based dish, 27mm Thermo ScientificTM Cat#150682 Microscope circular cover glass, thickness No.1.5, 25mm diameter Marienfeld Superior, Germany Cat#0112650 Microscope cover glass, thickness No.1.5 size: 24x50 mm Marienfeld Superior, Germany Cat#0102222 0.5mm Zirconia/Silica beads Biospec Products Cat#110791052 HisTrap HP column Cytiva Product No: 17524802 HiLoad 16/600 Superdex 200 pg column Cytiva Product No: 28989335 Superdex 200 Increase 10/300 GL column Cytiva Product No: 28990944 Amicon Ultra-15 Centrifugal Filter Unit Merk Millipore Cat#UFC901024 HiPrep 16/60 Sephacryl S-300 HR column Cytiva Product No: 17116701 Carbon support film 200 Mesh, copper Electron Microscopy Sciences Cat#CF200-Cu 1mm path length cuvette Hellma Analytics Article No:100-1-40 TLA-100 Fixed-Angle Rotor Beckman Coulter 343840 Plastic flow cell chamber (sticky-slide VI0.4) Ibidi GmbH Cat#80608

Article Title: The β-chain mutation p.Trp433Stop impairs fibrinogen secretion: A novel nonsense mutation associated with hypofibrinogenemia.
Article Snippet: Fibrinogen, a hexameric glycoprotein composed of Aα, Bβ, and γ chains, is the most abundant clotting factor in human circulation, and it has a multitude of functions, including platelet aggregation, primary and secondary hemostasis, and fibrinolysis.1 Congenital fibrinogen disorders are divided into two categories: type I, consisting of quantitative defects (afibrinogenemia or hypofibrinogenemia) characterized by absent or low plasma fibrinogen antigen and activity levels, and type II, consisting of qualitative defects Received: 8 December 2020 | Revised: 12 May 2021 | Accepted: 27 May 2021 DOI: 10.1111/ijlh.13632

Article Title: Protocol to identify multiple protein targets and therapeutic compounds using an in silico polypharmacological approach
Article Snippet: SWISS PDB Viewer , SIB Swiss Institute of Bioinformatics , https://spdbv.unil.ch/refs.html.

Article Title: Hexameric tetrahedral RNA nanostructures
Article Snippet: A three-dimensional model of the tetrahedral scaffold was manually constructed using SWISS PDB-VIEWER (The SIB Swiss Institute of Bioinformatics, available on the website for ExPASy Bioinformatics Resource Portal) and existing RNA structural data available in the PDB.

Article Title: Ubiquitin Modification by the E3 Ligase/ADP-ribosyltransferase Dtx3L/Parp9
Article Snippet: Swiss-PDB Viewer , The SIB Swiss Institute of Bioinformatics , N/A.

Article Title: A novel fibrinogen gamma-chain mutation, p.Cys165Arg, causes disruption of the γ165Cys-Bβ227Cys disulfide bond and ultimately leads to hypofibrinogenemia.
Article Snippet: Background: Congenital hypofibrinogenemia is a type of hereditary disease characterized by impaired fibrinogen synthesis and/or secretion induced by mutations in the fibrinogen gene.. Objectives: We investigated the phenotypes, genotypes, and pathogenesis of congenital hypofibrinogenemia in

Article Title: Genetic analysis of a pedigree with hereditary coagulation factor XI deficiency
Article Snippet: To identify potential mutations of F11 gene in a family with hereditary coagulation factor XI (FXI) deficiency and explore the molecular pathogenesis.. The FXI activity and FXI antigen were tested with clotting assay and ELISA, respectively.. The FXI gene was amplified by PCR with direct sequencing.

Virus:

Article Title: Hexameric tetrahedral RNA nanostructures
Article Snippet: A UA-handle three way junction (Protein Database (PDB) identification: 2AW4; nts 2090-2095, 2194-2201, 2220-2229) was then inserted into appropriate ring monomers, after which a helical segment was inserted to connect the junctions using SWISS PDB-VIEWER (The SIB Swiss Institute of Bioinformatics, available on the website for ExPASy Bioinformatics Resource Portal).

Article Title: The intrinsically disordered region of coronins fine-tunes oligomerization and actin polymerization.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Gromacs 5.1.2 Open source http://www.gromacs.org/ Swiss-Pdb Viewer (aka DeepView) SIB Swiss Institute of Bioinformatics http://www.expasy.org/spdbv/ CCBuilder 2.0 Open source http://coiledcoils.chm.bris.ac.uk/ ccbuilder2/builder PyMOL Schrödinger https://www.pymol.org/ Python for file processing CWI, the Netherlands https://www.python.org/ MATLAB vR2020b The MathWorks, Natick, MA https://www.mathworks.com/ PULCHRA Open Source http://cssb.bio.ogy.gatech.edu/skolnick/ files/PULCHRA Other Glass based dish, 27mm Thermo ScientificTM Cat#150682 Microscope circular cover glass, thickness No.1.5, 25mm diameter Marienfeld Superior, Germany Cat#0112650 Microscope cover glass, thickness No.1.5 size: 24x50 mm Marienfeld Superior, Germany Cat#0102222 0.5mm Zirconia/Silica beads Biospec Products Cat#110791052 HisTrap HP column Cytiva Product No: 17524802 HiLoad 16/600 Superdex 200 pg column Cytiva Product No: 28989335 Superdex 200 Increase 10/300 GL column Cytiva Product No: 28990944 Amicon Ultra-15 Centrifugal Filter Unit Merk Millipore Cat#UFC901024 HiPrep 16/60 Sephacryl S-300 HR column Cytiva Product No: 17116701 Carbon support film 200 Mesh, copper Electron Microscopy Sciences Cat#CF200-Cu 1mm path length cuvette Hellma Analytics Article No:100-1-40 TLA-100 Fixed-Angle Rotor Beckman Coulter 343840 Plastic flow cell chamber (sticky-slide VI0.4) Ibidi GmbH Cat#80608

Article Title: The β-chain mutation p.Trp433Stop impairs fibrinogen secretion: A novel nonsense mutation associated with hypofibrinogenemia.
Article Snippet: Fibrinogen, a hexameric glycoprotein composed of Aα, Bβ, and γ chains, is the most abundant clotting factor in human circulation, and it has a multitude of functions, including platelet aggregation, primary and secondary hemostasis, and fibrinolysis.1 Congenital fibrinogen disorders are divided into two categories: type I, consisting of quantitative defects (afibrinogenemia or hypofibrinogenemia) characterized by absent or low plasma fibrinogen antigen and activity levels, and type II, consisting of qualitative defects Received: 8 December 2020 | Revised: 12 May 2021 | Accepted: 27 May 2021 DOI: 10.1111/ijlh.13632

Article Title: Protocol to identify multiple protein targets and therapeutic compounds using an in silico polypharmacological approach
Article Snippet: SWISS PDB Viewer , SIB Swiss Institute of Bioinformatics , https://spdbv.unil.ch/refs.html.

Article Title: Hexameric tetrahedral RNA nanostructures
Article Snippet: A three-dimensional model of the tetrahedral scaffold was manually constructed using SWISS PDB-VIEWER (The SIB Swiss Institute of Bioinformatics, available on the website for ExPASy Bioinformatics Resource Portal) and existing RNA structural data available in the PDB.

Article Title: Ubiquitin Modification by the E3 Ligase/ADP-ribosyltransferase Dtx3L/Parp9
Article Snippet: Swiss-PDB Viewer , The SIB Swiss Institute of Bioinformatics , N/A.

Article Title: A novel fibrinogen gamma-chain mutation, p.Cys165Arg, causes disruption of the γ165Cys-Bβ227Cys disulfide bond and ultimately leads to hypofibrinogenemia.
Article Snippet: Background: Congenital hypofibrinogenemia is a type of hereditary disease characterized by impaired fibrinogen synthesis and/or secretion induced by mutations in the fibrinogen gene.. Objectives: We investigated the phenotypes, genotypes, and pathogenesis of congenital hypofibrinogenemia in

Article Title: Genetic analysis of a pedigree with hereditary coagulation factor XI deficiency
Article Snippet: To identify potential mutations of F11 gene in a family with hereditary coagulation factor XI (FXI) deficiency and explore the molecular pathogenesis.. The FXI activity and FXI antigen were tested with clotting assay and ELISA, respectively.. The FXI gene was amplified by PCR with direct sequencing.

Plasmid Preparation:

Article Title: Hexameric tetrahedral RNA nanostructures
Article Snippet: A UA-handle three way junction (Protein Database (PDB) identification: 2AW4; nts 2090-2095, 2194-2201, 2220-2229) was then inserted into appropriate ring monomers, after which a helical segment was inserted to connect the junctions using SWISS PDB-VIEWER (The SIB Swiss Institute of Bioinformatics, available on the website for ExPASy Bioinformatics Resource Portal).

Article Title: The intrinsically disordered region of coronins fine-tunes oligomerization and actin polymerization.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Gromacs 5.1.2 Open source http://www.gromacs.org/ Swiss-Pdb Viewer (aka DeepView) SIB Swiss Institute of Bioinformatics http://www.expasy.org/spdbv/ CCBuilder 2.0 Open source http://coiledcoils.chm.bris.ac.uk/ ccbuilder2/builder PyMOL Schrödinger https://www.pymol.org/ Python for file processing CWI, the Netherlands https://www.python.org/ MATLAB vR2020b The MathWorks, Natick, MA https://www.mathworks.com/ PULCHRA Open Source http://cssb.bio.ogy.gatech.edu/skolnick/ files/PULCHRA Other Glass based dish, 27mm Thermo ScientificTM Cat#150682 Microscope circular cover glass, thickness No.1.5, 25mm diameter Marienfeld Superior, Germany Cat#0112650 Microscope cover glass, thickness No.1.5 size: 24x50 mm Marienfeld Superior, Germany Cat#0102222 0.5mm Zirconia/Silica beads Biospec Products Cat#110791052 HisTrap HP column Cytiva Product No: 17524802 HiLoad 16/600 Superdex 200 pg column Cytiva Product No: 28989335 Superdex 200 Increase 10/300 GL column Cytiva Product No: 28990944 Amicon Ultra-15 Centrifugal Filter Unit Merk Millipore Cat#UFC901024 HiPrep 16/60 Sephacryl S-300 HR column Cytiva Product No: 17116701 Carbon support film 200 Mesh, copper Electron Microscopy Sciences Cat#CF200-Cu 1mm path length cuvette Hellma Analytics Article No:100-1-40 TLA-100 Fixed-Angle Rotor Beckman Coulter 343840 Plastic flow cell chamber (sticky-slide VI0.4) Ibidi GmbH Cat#80608

Article Title: The β-chain mutation p.Trp433Stop impairs fibrinogen secretion: A novel nonsense mutation associated with hypofibrinogenemia.
Article Snippet: Fibrinogen, a hexameric glycoprotein composed of Aα, Bβ, and γ chains, is the most abundant clotting factor in human circulation, and it has a multitude of functions, including platelet aggregation, primary and secondary hemostasis, and fibrinolysis.1 Congenital fibrinogen disorders are divided into two categories: type I, consisting of quantitative defects (afibrinogenemia or hypofibrinogenemia) characterized by absent or low plasma fibrinogen antigen and activity levels, and type II, consisting of qualitative defects Received: 8 December 2020 | Revised: 12 May 2021 | Accepted: 27 May 2021 DOI: 10.1111/ijlh.13632

Article Title: Protocol to identify multiple protein targets and therapeutic compounds using an in silico polypharmacological approach
Article Snippet: SWISS PDB Viewer , SIB Swiss Institute of Bioinformatics , https://spdbv.unil.ch/refs.html.

Article Title: Hexameric tetrahedral RNA nanostructures
Article Snippet: A three-dimensional model of the tetrahedral scaffold was manually constructed using SWISS PDB-VIEWER (The SIB Swiss Institute of Bioinformatics, available on the website for ExPASy Bioinformatics Resource Portal) and existing RNA structural data available in the PDB.

Article Title: Ubiquitin Modification by the E3 Ligase/ADP-ribosyltransferase Dtx3L/Parp9
Article Snippet: Swiss-PDB Viewer , The SIB Swiss Institute of Bioinformatics , N/A.

Article Title: A novel fibrinogen gamma-chain mutation, p.Cys165Arg, causes disruption of the γ165Cys-Bβ227Cys disulfide bond and ultimately leads to hypofibrinogenemia.
Article Snippet: Background: Congenital hypofibrinogenemia is a type of hereditary disease characterized by impaired fibrinogen synthesis and/or secretion induced by mutations in the fibrinogen gene.. Objectives: We investigated the phenotypes, genotypes, and pathogenesis of congenital hypofibrinogenemia in

Article Title: Genetic analysis of a pedigree with hereditary coagulation factor XI deficiency
Article Snippet: To identify potential mutations of F11 gene in a family with hereditary coagulation factor XI (FXI) deficiency and explore the molecular pathogenesis.. The FXI activity and FXI antigen were tested with clotting assay and ELISA, respectively.. The FXI gene was amplified by PCR with direct sequencing.

Recombinant:

Article Title: Hexameric tetrahedral RNA nanostructures
Article Snippet: A UA-handle three way junction (Protein Database (PDB) identification: 2AW4; nts 2090-2095, 2194-2201, 2220-2229) was then inserted into appropriate ring monomers, after which a helical segment was inserted to connect the junctions using SWISS PDB-VIEWER (The SIB Swiss Institute of Bioinformatics, available on the website for ExPASy Bioinformatics Resource Portal).

Article Title: The intrinsically disordered region of coronins fine-tunes oligomerization and actin polymerization.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Gromacs 5.1.2 Open source http://www.gromacs.org/ Swiss-Pdb Viewer (aka DeepView) SIB Swiss Institute of Bioinformatics http://www.expasy.org/spdbv/ CCBuilder 2.0 Open source http://coiledcoils.chm.bris.ac.uk/ ccbuilder2/builder PyMOL Schrödinger https://www.pymol.org/ Python for file processing CWI, the Netherlands https://www.python.org/ MATLAB vR2020b The MathWorks, Natick, MA https://www.mathworks.com/ PULCHRA Open Source http://cssb.bio.ogy.gatech.edu/skolnick/ files/PULCHRA Other Glass based dish, 27mm Thermo ScientificTM Cat#150682 Microscope circular cover glass, thickness No.1.5, 25mm diameter Marienfeld Superior, Germany Cat#0112650 Microscope cover glass, thickness No.1.5 size: 24x50 mm Marienfeld Superior, Germany Cat#0102222 0.5mm Zirconia/Silica beads Biospec Products Cat#110791052 HisTrap HP column Cytiva Product No: 17524802 HiLoad 16/600 Superdex 200 pg column Cytiva Product No: 28989335 Superdex 200 Increase 10/300 GL column Cytiva Product No: 28990944 Amicon Ultra-15 Centrifugal Filter Unit Merk Millipore Cat#UFC901024 HiPrep 16/60 Sephacryl S-300 HR column Cytiva Product No: 17116701 Carbon support film 200 Mesh, copper Electron Microscopy Sciences Cat#CF200-Cu 1mm path length cuvette Hellma Analytics Article No:100-1-40 TLA-100 Fixed-Angle Rotor Beckman Coulter 343840 Plastic flow cell chamber (sticky-slide VI0.4) Ibidi GmbH Cat#80608

Article Title: The β-chain mutation p.Trp433Stop impairs fibrinogen secretion: A novel nonsense mutation associated with hypofibrinogenemia.
Article Snippet: Fibrinogen, a hexameric glycoprotein composed of Aα, Bβ, and γ chains, is the most abundant clotting factor in human circulation, and it has a multitude of functions, including platelet aggregation, primary and secondary hemostasis, and fibrinolysis.1 Congenital fibrinogen disorders are divided into two categories: type I, consisting of quantitative defects (afibrinogenemia or hypofibrinogenemia) characterized by absent or low plasma fibrinogen antigen and activity levels, and type II, consisting of qualitative defects Received: 8 December 2020 | Revised: 12 May 2021 | Accepted: 27 May 2021 DOI: 10.1111/ijlh.13632

Article Title: Protocol to identify multiple protein targets and therapeutic compounds using an in silico polypharmacological approach
Article Snippet: SWISS PDB Viewer , SIB Swiss Institute of Bioinformatics , https://spdbv.unil.ch/refs.html.

Article Title: Hexameric tetrahedral RNA nanostructures
Article Snippet: A three-dimensional model of the tetrahedral scaffold was manually constructed using SWISS PDB-VIEWER (The SIB Swiss Institute of Bioinformatics, available on the website for ExPASy Bioinformatics Resource Portal) and existing RNA structural data available in the PDB.

Article Title: Ubiquitin Modification by the E3 Ligase/ADP-ribosyltransferase Dtx3L/Parp9
Article Snippet: Swiss-PDB Viewer , The SIB Swiss Institute of Bioinformatics , N/A.

Article Title: A novel fibrinogen gamma-chain mutation, p.Cys165Arg, causes disruption of the γ165Cys-Bβ227Cys disulfide bond and ultimately leads to hypofibrinogenemia.
Article Snippet: Background: Congenital hypofibrinogenemia is a type of hereditary disease characterized by impaired fibrinogen synthesis and/or secretion induced by mutations in the fibrinogen gene.. Objectives: We investigated the phenotypes, genotypes, and pathogenesis of congenital hypofibrinogenemia in

Article Title: Genetic analysis of a pedigree with hereditary coagulation factor XI deficiency
Article Snippet: To identify potential mutations of F11 gene in a family with hereditary coagulation factor XI (FXI) deficiency and explore the molecular pathogenesis.. The FXI activity and FXI antigen were tested with clotting assay and ELISA, respectively.. The FXI gene was amplified by PCR with direct sequencing.

TNKS1 Histone Ribosylation Assay:

Article Title: Hexameric tetrahedral RNA nanostructures
Article Snippet: A UA-handle three way junction (Protein Database (PDB) identification: 2AW4; nts 2090-2095, 2194-2201, 2220-2229) was then inserted into appropriate ring monomers, after which a helical segment was inserted to connect the junctions using SWISS PDB-VIEWER (The SIB Swiss Institute of Bioinformatics, available on the website for ExPASy Bioinformatics Resource Portal).

Article Title: The intrinsically disordered region of coronins fine-tunes oligomerization and actin polymerization.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Gromacs 5.1.2 Open source http://www.gromacs.org/ Swiss-Pdb Viewer (aka DeepView) SIB Swiss Institute of Bioinformatics http://www.expasy.org/spdbv/ CCBuilder 2.0 Open source http://coiledcoils.chm.bris.ac.uk/ ccbuilder2/builder PyMOL Schrödinger https://www.pymol.org/ Python for file processing CWI, the Netherlands https://www.python.org/ MATLAB vR2020b The MathWorks, Natick, MA https://www.mathworks.com/ PULCHRA Open Source http://cssb.bio.ogy.gatech.edu/skolnick/ files/PULCHRA Other Glass based dish, 27mm Thermo ScientificTM Cat#150682 Microscope circular cover glass, thickness No.1.5, 25mm diameter Marienfeld Superior, Germany Cat#0112650 Microscope cover glass, thickness No.1.5 size: 24x50 mm Marienfeld Superior, Germany Cat#0102222 0.5mm Zirconia/Silica beads Biospec Products Cat#110791052 HisTrap HP column Cytiva Product No: 17524802 HiLoad 16/600 Superdex 200 pg column Cytiva Product No: 28989335 Superdex 200 Increase 10/300 GL column Cytiva Product No: 28990944 Amicon Ultra-15 Centrifugal Filter Unit Merk Millipore Cat#UFC901024 HiPrep 16/60 Sephacryl S-300 HR column Cytiva Product No: 17116701 Carbon support film 200 Mesh, copper Electron Microscopy Sciences Cat#CF200-Cu 1mm path length cuvette Hellma Analytics Article No:100-1-40 TLA-100 Fixed-Angle Rotor Beckman Coulter 343840 Plastic flow cell chamber (sticky-slide VI0.4) Ibidi GmbH Cat#80608

Article Title: The β-chain mutation p.Trp433Stop impairs fibrinogen secretion: A novel nonsense mutation associated with hypofibrinogenemia.
Article Snippet: Fibrinogen, a hexameric glycoprotein composed of Aα, Bβ, and γ chains, is the most abundant clotting factor in human circulation, and it has a multitude of functions, including platelet aggregation, primary and secondary hemostasis, and fibrinolysis.1 Congenital fibrinogen disorders are divided into two categories: type I, consisting of quantitative defects (afibrinogenemia or hypofibrinogenemia) characterized by absent or low plasma fibrinogen antigen and activity levels, and type II, consisting of qualitative defects Received: 8 December 2020 | Revised: 12 May 2021 | Accepted: 27 May 2021 DOI: 10.1111/ijlh.13632

Article Title: Protocol to identify multiple protein targets and therapeutic compounds using an in silico polypharmacological approach
Article Snippet: SWISS PDB Viewer , SIB Swiss Institute of Bioinformatics , https://spdbv.unil.ch/refs.html.

Article Title: Hexameric tetrahedral RNA nanostructures
Article Snippet: A three-dimensional model of the tetrahedral scaffold was manually constructed using SWISS PDB-VIEWER (The SIB Swiss Institute of Bioinformatics, available on the website for ExPASy Bioinformatics Resource Portal) and existing RNA structural data available in the PDB.

Article Title: Ubiquitin Modification by the E3 Ligase/ADP-ribosyltransferase Dtx3L/Parp9
Article Snippet: Swiss-PDB Viewer , The SIB Swiss Institute of Bioinformatics , N/A.

Article Title: A novel fibrinogen gamma-chain mutation, p.Cys165Arg, causes disruption of the γ165Cys-Bβ227Cys disulfide bond and ultimately leads to hypofibrinogenemia.
Article Snippet: Background: Congenital hypofibrinogenemia is a type of hereditary disease characterized by impaired fibrinogen synthesis and/or secretion induced by mutations in the fibrinogen gene.. Objectives: We investigated the phenotypes, genotypes, and pathogenesis of congenital hypofibrinogenemia in

Article Title: Genetic analysis of a pedigree with hereditary coagulation factor XI deficiency
Article Snippet: To identify potential mutations of F11 gene in a family with hereditary coagulation factor XI (FXI) deficiency and explore the molecular pathogenesis.. The FXI activity and FXI antigen were tested with clotting assay and ELISA, respectively.. The FXI gene was amplified by PCR with direct sequencing.

Sequencing:

Article Title: Hexameric tetrahedral RNA nanostructures
Article Snippet: A UA-handle three way junction (Protein Database (PDB) identification: 2AW4; nts 2090-2095, 2194-2201, 2220-2229) was then inserted into appropriate ring monomers, after which a helical segment was inserted to connect the junctions using SWISS PDB-VIEWER (The SIB Swiss Institute of Bioinformatics, available on the website for ExPASy Bioinformatics Resource Portal).

Article Title: The intrinsically disordered region of coronins fine-tunes oligomerization and actin polymerization.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Gromacs 5.1.2 Open source http://www.gromacs.org/ Swiss-Pdb Viewer (aka DeepView) SIB Swiss Institute of Bioinformatics http://www.expasy.org/spdbv/ CCBuilder 2.0 Open source http://coiledcoils.chm.bris.ac.uk/ ccbuilder2/builder PyMOL Schrödinger https://www.pymol.org/ Python for file processing CWI, the Netherlands https://www.python.org/ MATLAB vR2020b The MathWorks, Natick, MA https://www.mathworks.com/ PULCHRA Open Source http://cssb.bio.ogy.gatech.edu/skolnick/ files/PULCHRA Other Glass based dish, 27mm Thermo ScientificTM Cat#150682 Microscope circular cover glass, thickness No.1.5, 25mm diameter Marienfeld Superior, Germany Cat#0112650 Microscope cover glass, thickness No.1.5 size: 24x50 mm Marienfeld Superior, Germany Cat#0102222 0.5mm Zirconia/Silica beads Biospec Products Cat#110791052 HisTrap HP column Cytiva Product No: 17524802 HiLoad 16/600 Superdex 200 pg column Cytiva Product No: 28989335 Superdex 200 Increase 10/300 GL column Cytiva Product No: 28990944 Amicon Ultra-15 Centrifugal Filter Unit Merk Millipore Cat#UFC901024 HiPrep 16/60 Sephacryl S-300 HR column Cytiva Product No: 17116701 Carbon support film 200 Mesh, copper Electron Microscopy Sciences Cat#CF200-Cu 1mm path length cuvette Hellma Analytics Article No:100-1-40 TLA-100 Fixed-Angle Rotor Beckman Coulter 343840 Plastic flow cell chamber (sticky-slide VI0.4) Ibidi GmbH Cat#80608

Article Title: The β-chain mutation p.Trp433Stop impairs fibrinogen secretion: A novel nonsense mutation associated with hypofibrinogenemia.
Article Snippet: Fibrinogen, a hexameric glycoprotein composed of Aα, Bβ, and γ chains, is the most abundant clotting factor in human circulation, and it has a multitude of functions, including platelet aggregation, primary and secondary hemostasis, and fibrinolysis.1 Congenital fibrinogen disorders are divided into two categories: type I, consisting of quantitative defects (afibrinogenemia or hypofibrinogenemia) characterized by absent or low plasma fibrinogen antigen and activity levels, and type II, consisting of qualitative defects Received: 8 December 2020 | Revised: 12 May 2021 | Accepted: 27 May 2021 DOI: 10.1111/ijlh.13632

Article Title: Protocol to identify multiple protein targets and therapeutic compounds using an in silico polypharmacological approach
Article Snippet: SWISS PDB Viewer , SIB Swiss Institute of Bioinformatics , https://spdbv.unil.ch/refs.html.

Article Title: Hexameric tetrahedral RNA nanostructures
Article Snippet: A three-dimensional model of the tetrahedral scaffold was manually constructed using SWISS PDB-VIEWER (The SIB Swiss Institute of Bioinformatics, available on the website for ExPASy Bioinformatics Resource Portal) and existing RNA structural data available in the PDB.

Article Title: Ubiquitin Modification by the E3 Ligase/ADP-ribosyltransferase Dtx3L/Parp9
Article Snippet: Swiss-PDB Viewer , The SIB Swiss Institute of Bioinformatics , N/A.

Article Title: A novel fibrinogen gamma-chain mutation, p.Cys165Arg, causes disruption of the γ165Cys-Bβ227Cys disulfide bond and ultimately leads to hypofibrinogenemia.
Article Snippet: Background: Congenital hypofibrinogenemia is a type of hereditary disease characterized by impaired fibrinogen synthesis and/or secretion induced by mutations in the fibrinogen gene.. Objectives: We investigated the phenotypes, genotypes, and pathogenesis of congenital hypofibrinogenemia in

Article Title: Genetic analysis of a pedigree with hereditary coagulation factor XI deficiency
Article Snippet: To identify potential mutations of F11 gene in a family with hereditary coagulation factor XI (FXI) deficiency and explore the molecular pathogenesis.. The FXI activity and FXI antigen were tested with clotting assay and ELISA, respectively.. The FXI gene was amplified by PCR with direct sequencing.

Control:

Article Title: Hexameric tetrahedral RNA nanostructures
Article Snippet: A UA-handle three way junction (Protein Database (PDB) identification: 2AW4; nts 2090-2095, 2194-2201, 2220-2229) was then inserted into appropriate ring monomers, after which a helical segment was inserted to connect the junctions using SWISS PDB-VIEWER (The SIB Swiss Institute of Bioinformatics, available on the website for ExPASy Bioinformatics Resource Portal).

Article Title: The intrinsically disordered region of coronins fine-tunes oligomerization and actin polymerization.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Gromacs 5.1.2 Open source http://www.gromacs.org/ Swiss-Pdb Viewer (aka DeepView) SIB Swiss Institute of Bioinformatics http://www.expasy.org/spdbv/ CCBuilder 2.0 Open source http://coiledcoils.chm.bris.ac.uk/ ccbuilder2/builder PyMOL Schrödinger https://www.pymol.org/ Python for file processing CWI, the Netherlands https://www.python.org/ MATLAB vR2020b The MathWorks, Natick, MA https://www.mathworks.com/ PULCHRA Open Source http://cssb.bio.ogy.gatech.edu/skolnick/ files/PULCHRA Other Glass based dish, 27mm Thermo ScientificTM Cat#150682 Microscope circular cover glass, thickness No.1.5, 25mm diameter Marienfeld Superior, Germany Cat#0112650 Microscope cover glass, thickness No.1.5 size: 24x50 mm Marienfeld Superior, Germany Cat#0102222 0.5mm Zirconia/Silica beads Biospec Products Cat#110791052 HisTrap HP column Cytiva Product No: 17524802 HiLoad 16/600 Superdex 200 pg column Cytiva Product No: 28989335 Superdex 200 Increase 10/300 GL column Cytiva Product No: 28990944 Amicon Ultra-15 Centrifugal Filter Unit Merk Millipore Cat#UFC901024 HiPrep 16/60 Sephacryl S-300 HR column Cytiva Product No: 17116701 Carbon support film 200 Mesh, copper Electron Microscopy Sciences Cat#CF200-Cu 1mm path length cuvette Hellma Analytics Article No:100-1-40 TLA-100 Fixed-Angle Rotor Beckman Coulter 343840 Plastic flow cell chamber (sticky-slide VI0.4) Ibidi GmbH Cat#80608

Article Title: The β-chain mutation p.Trp433Stop impairs fibrinogen secretion: A novel nonsense mutation associated with hypofibrinogenemia.
Article Snippet: Fibrinogen, a hexameric glycoprotein composed of Aα, Bβ, and γ chains, is the most abundant clotting factor in human circulation, and it has a multitude of functions, including platelet aggregation, primary and secondary hemostasis, and fibrinolysis.1 Congenital fibrinogen disorders are divided into two categories: type I, consisting of quantitative defects (afibrinogenemia or hypofibrinogenemia) characterized by absent or low plasma fibrinogen antigen and activity levels, and type II, consisting of qualitative defects Received: 8 December 2020 | Revised: 12 May 2021 | Accepted: 27 May 2021 DOI: 10.1111/ijlh.13632

Article Title: Protocol to identify multiple protein targets and therapeutic compounds using an in silico polypharmacological approach
Article Snippet: SWISS PDB Viewer , SIB Swiss Institute of Bioinformatics , https://spdbv.unil.ch/refs.html.

Article Title: Hexameric tetrahedral RNA nanostructures
Article Snippet: A three-dimensional model of the tetrahedral scaffold was manually constructed using SWISS PDB-VIEWER (The SIB Swiss Institute of Bioinformatics, available on the website for ExPASy Bioinformatics Resource Portal) and existing RNA structural data available in the PDB.

Article Title: Ubiquitin Modification by the E3 Ligase/ADP-ribosyltransferase Dtx3L/Parp9
Article Snippet: Swiss-PDB Viewer , The SIB Swiss Institute of Bioinformatics , N/A.

Article Title: A novel fibrinogen gamma-chain mutation, p.Cys165Arg, causes disruption of the γ165Cys-Bβ227Cys disulfide bond and ultimately leads to hypofibrinogenemia.
Article Snippet: Background: Congenital hypofibrinogenemia is a type of hereditary disease characterized by impaired fibrinogen synthesis and/or secretion induced by mutations in the fibrinogen gene.. Objectives: We investigated the phenotypes, genotypes, and pathogenesis of congenital hypofibrinogenemia in

Article Title: Genetic analysis of a pedigree with hereditary coagulation factor XI deficiency
Article Snippet: To identify potential mutations of F11 gene in a family with hereditary coagulation factor XI (FXI) deficiency and explore the molecular pathogenesis.. The FXI activity and FXI antigen were tested with clotting assay and ELISA, respectively.. The FXI gene was amplified by PCR with direct sequencing.

Flow Cytometry:

Article Title: Hexameric tetrahedral RNA nanostructures
Article Snippet: A UA-handle three way junction (Protein Database (PDB) identification: 2AW4; nts 2090-2095, 2194-2201, 2220-2229) was then inserted into appropriate ring monomers, after which a helical segment was inserted to connect the junctions using SWISS PDB-VIEWER (The SIB Swiss Institute of Bioinformatics, available on the website for ExPASy Bioinformatics Resource Portal).

Article Title: The intrinsically disordered region of coronins fine-tunes oligomerization and actin polymerization.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Gromacs 5.1.2 Open source http://www.gromacs.org/ Swiss-Pdb Viewer (aka DeepView) SIB Swiss Institute of Bioinformatics http://www.expasy.org/spdbv/ CCBuilder 2.0 Open source http://coiledcoils.chm.bris.ac.uk/ ccbuilder2/builder PyMOL Schrödinger https://www.pymol.org/ Python for file processing CWI, the Netherlands https://www.python.org/ MATLAB vR2020b The MathWorks, Natick, MA https://www.mathworks.com/ PULCHRA Open Source http://cssb.bio.ogy.gatech.edu/skolnick/ files/PULCHRA Other Glass based dish, 27mm Thermo ScientificTM Cat#150682 Microscope circular cover glass, thickness No.1.5, 25mm diameter Marienfeld Superior, Germany Cat#0112650 Microscope cover glass, thickness No.1.5 size: 24x50 mm Marienfeld Superior, Germany Cat#0102222 0.5mm Zirconia/Silica beads Biospec Products Cat#110791052 HisTrap HP column Cytiva Product No: 17524802 HiLoad 16/600 Superdex 200 pg column Cytiva Product No: 28989335 Superdex 200 Increase 10/300 GL column Cytiva Product No: 28990944 Amicon Ultra-15 Centrifugal Filter Unit Merk Millipore Cat#UFC901024 HiPrep 16/60 Sephacryl S-300 HR column Cytiva Product No: 17116701 Carbon support film 200 Mesh, copper Electron Microscopy Sciences Cat#CF200-Cu 1mm path length cuvette Hellma Analytics Article No:100-1-40 TLA-100 Fixed-Angle Rotor Beckman Coulter 343840 Plastic flow cell chamber (sticky-slide VI0.4) Ibidi GmbH Cat#80608

Article Title: The β-chain mutation p.Trp433Stop impairs fibrinogen secretion: A novel nonsense mutation associated with hypofibrinogenemia.
Article Snippet: Fibrinogen, a hexameric glycoprotein composed of Aα, Bβ, and γ chains, is the most abundant clotting factor in human circulation, and it has a multitude of functions, including platelet aggregation, primary and secondary hemostasis, and fibrinolysis.1 Congenital fibrinogen disorders are divided into two categories: type I, consisting of quantitative defects (afibrinogenemia or hypofibrinogenemia) characterized by absent or low plasma fibrinogen antigen and activity levels, and type II, consisting of qualitative defects Received: 8 December 2020 | Revised: 12 May 2021 | Accepted: 27 May 2021 DOI: 10.1111/ijlh.13632

Article Title: Protocol to identify multiple protein targets and therapeutic compounds using an in silico polypharmacological approach
Article Snippet: SWISS PDB Viewer , SIB Swiss Institute of Bioinformatics , https://spdbv.unil.ch/refs.html.

Article Title: Hexameric tetrahedral RNA nanostructures
Article Snippet: A three-dimensional model of the tetrahedral scaffold was manually constructed using SWISS PDB-VIEWER (The SIB Swiss Institute of Bioinformatics, available on the website for ExPASy Bioinformatics Resource Portal) and existing RNA structural data available in the PDB.

Article Title: Ubiquitin Modification by the E3 Ligase/ADP-ribosyltransferase Dtx3L/Parp9
Article Snippet: Swiss-PDB Viewer , The SIB Swiss Institute of Bioinformatics , N/A.

Article Title: A novel fibrinogen gamma-chain mutation, p.Cys165Arg, causes disruption of the γ165Cys-Bβ227Cys disulfide bond and ultimately leads to hypofibrinogenemia.
Article Snippet: Background: Congenital hypofibrinogenemia is a type of hereditary disease characterized by impaired fibrinogen synthesis and/or secretion induced by mutations in the fibrinogen gene.. Objectives: We investigated the phenotypes, genotypes, and pathogenesis of congenital hypofibrinogenemia in

Article Title: Genetic analysis of a pedigree with hereditary coagulation factor XI deficiency
Article Snippet: To identify potential mutations of F11 gene in a family with hereditary coagulation factor XI (FXI) deficiency and explore the molecular pathogenesis.. The FXI activity and FXI antigen were tested with clotting assay and ELISA, respectively.. The FXI gene was amplified by PCR with direct sequencing.



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DeLano Scientific pymol software (python-based molecular visualization system)
Binding model of CHE19 to the CHIKV spike protein. (A) Amino acid (aa) sequence alignment (1 to 300 aa) using Blosum62 for E2 (423 aa) from the CHIKV Thai#16856, Thai/ES245-7, Ross, and Thai E2 mutants. Domains of E2 determined from the crystal structure of the E2/E1 heterodimer (16) are shown. Domains A, B, and C are shown in black with underlining, while the N-linker segment and 2 β-ribbon connectors, β-ribbon (1) and β-ribbon (2) are shown in purple. The amino acid residues of Thai#16856 came into contact within 4 Å from the heavy atoms of the paratopes of the CHE19, as in panel A-2, are shown in red. The positions where residues are replaced by alanine of the respective Thai E2 mutants, YKATR/AAATA, Thai/TTTDK/AAADA, HKKW/AAAA, and RQGK/AQGA, are shown in light blue. (B) Nucleotide and amino acid sequences of the Fab fragment region of the CHE19 light chain and heavy chain. PCR primer sequences are shown in red (sense) and blue (antisense). The signal peptide sequence of each chain is highlighted in yellow. Variable regions of the light chain and heavy chain are highlighted in light blue and blue, respectively. (C-1) Deduced binding model no. 16 of CHE19 to the CHIKV spike protein. Ribbon drawings of the spike with the bound Fab fragment of CHE19 and whole model of CHE19. The E1 glycoprotein is shown in red, the E2 glycoprotein in green, and the CHE19 Fab fragment region or whole Fab fragment plus Fc structure is shown in blue for the heavy chain and light blue for the light chain. The ribbon diagram of the spike protein was reconstructed by HMHC using PDB ID 6NK7, and the ribbon diagrams of CHE19 Fab fragment and Fab fragment-Fc were reconstructed using PDB IDs 5TL5 and 5TL5 to 1IGT, respectively. (C-2) Blowup of the binding location with the amino acids (shown as spheres) that are in contact within 4 Å from the heavy atoms of the paratopes of the CHE19 region. (C-3) The binding of CHE19 Fab fragment (translucent surface drawings: blue for the heavy chain and light blue for the light chain) on the E2-E1 heterodimer (E2, green ribbon; E1, red ribbon) overlapped the position where the E3 glycoprotein (pink ribbon) was originally occupied. The fusion loop located at the distal end of the E1 glycoprotein is shown in yellow. The ribbon diagrams of the E2-E1 heterodimer in panels C-2 and C-3 were reconstructed by HMHC using PDB ID 3N42. (C-4) Structural image showing that the CHE19 (surface drawings: blue for the heavy chain and light blue for the light chain) connects the CHIKV virion by binding to the spike protein (brown ribbon) existing on two different virions. The ribbon diagrams of structural proteins are reconstructed by HMHC using PDB ID 6NK7. The ratio between virion size and spike size was determined with reference to the mature CHIKV structure model (51). These images were visualized using the UCSF Chimera software (panels C-1, C-3, and C-4) and the <t>PyMOL</t> software (panel C-2). (D) Expression of CHIKV mutant E proteins and their detection by the respective MAbs. (D-1) MAb reactivities by IFA of 293T cells transfected with pCAGGS/CHIKV-E Thai#16856, pCAGGS/CHIKV-E Thai/ES245-7, and four pCAGGS/CHIKV mutant E expression plasmids, pCAGGS/CHIKV-E Thai/YKATR/AAATA, pCAGGS/CHIKV-E Thai/TTTDK/AAADA, pCAGGS/CHIKV-E Thai/HKKW/AAAA, and pCAGGS/CHIKV-E Thai/RQGK/AQGA, were probed with the respective MAbs and anti-CHIKV rabbit serum as a positive control. (D-2) Expression of CHIKV mutant E proteins in 293T cells transfected with the respective CHIKV-E-expressing vectors was detected by Western blotting using anti-CHIKV rabbit serum and two anti-CHIKV mouse IgGs, CHE15 and CHE22. The cellular beta-actin as an internal control was probed by anti-beta-actin mouse MAb (Sigma-Aldrich). (E) VSVΔG-luci pseudoviruses bearing the CHIKV-E protein of the Thai#16856, Thai/ES245-7, and Thai E2 mutants (YKATR/AAATA, TTTDK/AAADA, HKKW/AAAA, and RQGK/AQGA) were examined for their infectivity to Vero cells and their reactivity against CHE19. (E-1) Pseudotype viruses except VSVΔG-luci (CHIKV-E Thai E2 HKKW/AAAA) were produced, and their infectivity was inhibited by anti-CHIKV rabbit serum treatment (1:100). The infectivity of the respective pseudotype virus is shown as a percentage of the VSVΔG-luci (CHIKV-E Thai#16856) infectivity. (E-2) VSVΔG-luci (CHIKV-E Thai E2 YKATR/AAATA) was completely resistant against the CHE19 treatment (10 μg/ml), and VSVΔG-luci (CHIKV-E Thai E2 RQGK/AQGA) was partially resistant, but VSVΔG-luci (CHIKV-E Thai E2 TTTDK/AAADA) was neutralized to the same level as VSVΔG-luci (CHIKV-E Thai#16856). The infectivity of each pseudovirus is shown as a percentage of the infectivity of the respective pseudovirus treated with the Ctrl IgG. Data are the mean ± SEM (n = 6) of three independent experiments. Statistical significance was evaluated by an unpaired two-tailed t test. *, P < 0.05; **, P < 0.01; ***, P < 0.001; ****, P < 0.0001.
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Binding model of CHE19 to the CHIKV spike protein. (A) Amino acid (aa) sequence alignment (1 to 300 aa) using Blosum62 for E2 (423 aa) from the CHIKV Thai#16856, Thai/ES245-7, Ross, and Thai E2 mutants. Domains of E2 determined from the crystal structure of the E2/E1 heterodimer (16) are shown. Domains A, B, and C are shown in black with underlining, while the N-linker segment and 2 β-ribbon connectors, β-ribbon (1) and β-ribbon (2) are shown in purple. The amino acid residues of Thai#16856 came into contact within 4 Å from the heavy atoms of the paratopes of the CHE19, as in panel A-2, are shown in red. The positions where residues are replaced by alanine of the respective Thai E2 mutants, YKATR/AAATA, Thai/TTTDK/AAADA, HKKW/AAAA, and RQGK/AQGA, are shown in light blue. (B) Nucleotide and amino acid sequences of the Fab fragment region of the CHE19 light chain and heavy chain. PCR primer sequences are shown in red (sense) and blue (antisense). The signal peptide sequence of each chain is highlighted in yellow. Variable regions of the light chain and heavy chain are highlighted in light blue and blue, respectively. (C-1) Deduced binding model no. 16 of CHE19 to the CHIKV spike protein. Ribbon drawings of the spike with the bound Fab fragment of CHE19 and whole model of CHE19. The E1 glycoprotein is shown in red, the E2 glycoprotein in green, and the CHE19 Fab fragment region or whole Fab fragment plus Fc structure is shown in blue for the heavy chain and light blue for the light chain. The ribbon diagram of the spike protein was reconstructed by HMHC using PDB ID 6NK7, and the ribbon diagrams of CHE19 Fab fragment and Fab fragment-Fc were reconstructed using PDB IDs 5TL5 and 5TL5 to 1IGT, respectively. (C-2) Blowup of the binding location with the amino acids (shown as spheres) that are in contact within 4 Å from the heavy atoms of the paratopes of the CHE19 region. (C-3) The binding of CHE19 Fab fragment (translucent surface drawings: blue for the heavy chain and light blue for the light chain) on the E2-E1 heterodimer (E2, green ribbon; E1, red ribbon) overlapped the position where the E3 glycoprotein (pink ribbon) was originally occupied. The fusion loop located at the distal end of the E1 glycoprotein is shown in yellow. The ribbon diagrams of the E2-E1 heterodimer in panels C-2 and C-3 were reconstructed by HMHC using PDB ID 3N42. (C-4) Structural image showing that the CHE19 (surface drawings: blue for the heavy chain and light blue for the light chain) connects the CHIKV virion by binding to the spike protein (brown ribbon) existing on two different virions. The ribbon diagrams of structural proteins are reconstructed by HMHC using PDB ID 6NK7. The ratio between virion size and spike size was determined with reference to the mature CHIKV structure model (51). These images were visualized using the UCSF Chimera software (panels C-1, C-3, and C-4) and the PyMOL software (panel C-2). (D) Expression of CHIKV mutant E proteins and their detection by the respective MAbs. (D-1) MAb reactivities by IFA of 293T cells transfected with pCAGGS/CHIKV-E Thai#16856, pCAGGS/CHIKV-E Thai/ES245-7, and four pCAGGS/CHIKV mutant E expression plasmids, pCAGGS/CHIKV-E Thai/YKATR/AAATA, pCAGGS/CHIKV-E Thai/TTTDK/AAADA, pCAGGS/CHIKV-E Thai/HKKW/AAAA, and pCAGGS/CHIKV-E Thai/RQGK/AQGA, were probed with the respective MAbs and anti-CHIKV rabbit serum as a positive control. (D-2) Expression of CHIKV mutant E proteins in 293T cells transfected with the respective CHIKV-E-expressing vectors was detected by Western blotting using anti-CHIKV rabbit serum and two anti-CHIKV mouse IgGs, CHE15 and CHE22. The cellular beta-actin as an internal control was probed by anti-beta-actin mouse MAb (Sigma-Aldrich). (E) VSVΔG-luci pseudoviruses bearing the CHIKV-E protein of the Thai#16856, Thai/ES245-7, and Thai E2 mutants (YKATR/AAATA, TTTDK/AAADA, HKKW/AAAA, and RQGK/AQGA) were examined for their infectivity to Vero cells and their reactivity against CHE19. (E-1) Pseudotype viruses except VSVΔG-luci (CHIKV-E Thai E2 HKKW/AAAA) were produced, and their infectivity was inhibited by anti-CHIKV rabbit serum treatment (1:100). The infectivity of the respective pseudotype virus is shown as a percentage of the VSVΔG-luci (CHIKV-E Thai#16856) infectivity. (E-2) VSVΔG-luci (CHIKV-E Thai E2 YKATR/AAATA) was completely resistant against the CHE19 treatment (10 μg/ml), and VSVΔG-luci (CHIKV-E Thai E2 RQGK/AQGA) was partially resistant, but VSVΔG-luci (CHIKV-E Thai E2 TTTDK/AAADA) was neutralized to the same level as VSVΔG-luci (CHIKV-E Thai#16856). The infectivity of each pseudovirus is shown as a percentage of the infectivity of the respective pseudovirus treated with the Ctrl IgG. Data are the mean ± SEM (n = 6) of three independent experiments. Statistical significance was evaluated by an unpaired two-tailed t test. *, P < 0.05; **, P < 0.01; ***, P < 0.001; ****, P < 0.0001.

Journal: Journal of Virology

Article Title: Anti-Chikungunya Virus Monoclonal Antibody That Inhibits Viral Fusion and Release

doi: 10.1128/JVI.00252-20

Figure Lengend Snippet: Binding model of CHE19 to the CHIKV spike protein. (A) Amino acid (aa) sequence alignment (1 to 300 aa) using Blosum62 for E2 (423 aa) from the CHIKV Thai#16856, Thai/ES245-7, Ross, and Thai E2 mutants. Domains of E2 determined from the crystal structure of the E2/E1 heterodimer (16) are shown. Domains A, B, and C are shown in black with underlining, while the N-linker segment and 2 β-ribbon connectors, β-ribbon (1) and β-ribbon (2) are shown in purple. The amino acid residues of Thai#16856 came into contact within 4 Å from the heavy atoms of the paratopes of the CHE19, as in panel A-2, are shown in red. The positions where residues are replaced by alanine of the respective Thai E2 mutants, YKATR/AAATA, Thai/TTTDK/AAADA, HKKW/AAAA, and RQGK/AQGA, are shown in light blue. (B) Nucleotide and amino acid sequences of the Fab fragment region of the CHE19 light chain and heavy chain. PCR primer sequences are shown in red (sense) and blue (antisense). The signal peptide sequence of each chain is highlighted in yellow. Variable regions of the light chain and heavy chain are highlighted in light blue and blue, respectively. (C-1) Deduced binding model no. 16 of CHE19 to the CHIKV spike protein. Ribbon drawings of the spike with the bound Fab fragment of CHE19 and whole model of CHE19. The E1 glycoprotein is shown in red, the E2 glycoprotein in green, and the CHE19 Fab fragment region or whole Fab fragment plus Fc structure is shown in blue for the heavy chain and light blue for the light chain. The ribbon diagram of the spike protein was reconstructed by HMHC using PDB ID 6NK7, and the ribbon diagrams of CHE19 Fab fragment and Fab fragment-Fc were reconstructed using PDB IDs 5TL5 and 5TL5 to 1IGT, respectively. (C-2) Blowup of the binding location with the amino acids (shown as spheres) that are in contact within 4 Å from the heavy atoms of the paratopes of the CHE19 region. (C-3) The binding of CHE19 Fab fragment (translucent surface drawings: blue for the heavy chain and light blue for the light chain) on the E2-E1 heterodimer (E2, green ribbon; E1, red ribbon) overlapped the position where the E3 glycoprotein (pink ribbon) was originally occupied. The fusion loop located at the distal end of the E1 glycoprotein is shown in yellow. The ribbon diagrams of the E2-E1 heterodimer in panels C-2 and C-3 were reconstructed by HMHC using PDB ID 3N42. (C-4) Structural image showing that the CHE19 (surface drawings: blue for the heavy chain and light blue for the light chain) connects the CHIKV virion by binding to the spike protein (brown ribbon) existing on two different virions. The ribbon diagrams of structural proteins are reconstructed by HMHC using PDB ID 6NK7. The ratio between virion size and spike size was determined with reference to the mature CHIKV structure model (51). These images were visualized using the UCSF Chimera software (panels C-1, C-3, and C-4) and the PyMOL software (panel C-2). (D) Expression of CHIKV mutant E proteins and their detection by the respective MAbs. (D-1) MAb reactivities by IFA of 293T cells transfected with pCAGGS/CHIKV-E Thai#16856, pCAGGS/CHIKV-E Thai/ES245-7, and four pCAGGS/CHIKV mutant E expression plasmids, pCAGGS/CHIKV-E Thai/YKATR/AAATA, pCAGGS/CHIKV-E Thai/TTTDK/AAADA, pCAGGS/CHIKV-E Thai/HKKW/AAAA, and pCAGGS/CHIKV-E Thai/RQGK/AQGA, were probed with the respective MAbs and anti-CHIKV rabbit serum as a positive control. (D-2) Expression of CHIKV mutant E proteins in 293T cells transfected with the respective CHIKV-E-expressing vectors was detected by Western blotting using anti-CHIKV rabbit serum and two anti-CHIKV mouse IgGs, CHE15 and CHE22. The cellular beta-actin as an internal control was probed by anti-beta-actin mouse MAb (Sigma-Aldrich). (E) VSVΔG-luci pseudoviruses bearing the CHIKV-E protein of the Thai#16856, Thai/ES245-7, and Thai E2 mutants (YKATR/AAATA, TTTDK/AAADA, HKKW/AAAA, and RQGK/AQGA) were examined for their infectivity to Vero cells and their reactivity against CHE19. (E-1) Pseudotype viruses except VSVΔG-luci (CHIKV-E Thai E2 HKKW/AAAA) were produced, and their infectivity was inhibited by anti-CHIKV rabbit serum treatment (1:100). The infectivity of the respective pseudotype virus is shown as a percentage of the VSVΔG-luci (CHIKV-E Thai#16856) infectivity. (E-2) VSVΔG-luci (CHIKV-E Thai E2 YKATR/AAATA) was completely resistant against the CHE19 treatment (10 μg/ml), and VSVΔG-luci (CHIKV-E Thai E2 RQGK/AQGA) was partially resistant, but VSVΔG-luci (CHIKV-E Thai E2 TTTDK/AAADA) was neutralized to the same level as VSVΔG-luci (CHIKV-E Thai#16856). The infectivity of each pseudovirus is shown as a percentage of the infectivity of the respective pseudovirus treated with the Ctrl IgG. Data are the mean ± SEM (n = 6) of three independent experiments. Statistical significance was evaluated by an unpaired two-tailed t test. *, P < 0.05; **, P < 0.01; ***, P < 0.001; ****, P < 0.0001.

Article Snippet: The obtained docking models of the CHE19 Fab fragment-CHIKV E2-E1 complex were examined to confirm that the paratope of the antibody interacts with the antigen by PyMOL software (Python-based molecular visualization system; Delano Scientific, San Francisco, CA).

Techniques: Binding Assay, Sequencing, Software, Expressing, Mutagenesis, Transfection, Positive Control, Western Blot, Infection, Produced, Two Tailed Test